1
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Gomes JGDS, Brandão LC, Pinheiro DP, Pontes LQ, Carneiro RF, Quintela BCSF, Marinho ACM, Furtado GP, Rocha BAM. Kinetics characterization of a low immunogenic recombinant l-asparaginase from Phaseolus vulgaris with cytotoxic activity against leukemia cells. Int J Biol Macromol 2024; 275:133731. [PMID: 38986978 DOI: 10.1016/j.ijbiomac.2024.133731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/15/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
l-asparaginases play a crucial role in the treatment of acute lymphoblastic leukemia (ALL), a type of cancer that mostly affects children and teenagers. However, it is common for these molecules to cause adverse reactions during treatment. These downsides ignite the search for novel asparaginases to mitigate these problems. Thus, this work aimed to produce and characterize a recombinant asparaginase from Phaseolus vulgaris (Asp-P). In this study, Asp-P was expressed in Escherichia coli with high yields and optimum activity at 40 °C, pH 9.0. The enzyme Km and Vmax values were 7.05 mM and 1027 U/mg, respectively. Asp-P is specific for l-asparagine, showing no activity against l-glutamine and other amino acids. The enzyme showed a higher cytotoxic effect against Raji than K562 cell lines, but only at high concentrations. In silico analysis indicated that Asp-P has lower immunogenicity than a commercial enzyme. Asp-P induced biofilm formation by Candida sp. due to sublethal dose, showing an underexplored potential of asparaginases. The absence of glutaminase activity, lower immunogenicity and optimal activity similar to physiological temperature conditions are characteristics that indicate Asp-P as a potential new commercial enzyme in the treatment of ALL and its underexplored application in the treatment of other diseases.
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Affiliation(s)
| | - Larisse Cadeira Brandão
- Departament of Fishing Engineering, Federal University of Ceara, Fortaleza, Brazil; Oswaldo Cruz Foundation - Fiocruz Ceara, Eusebio, Ceara, Brazil
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2
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Jung MY, Baek CH, Ma Y, Lee HW. Acrylamide formation in air-fryer roasted legumes as affected by legume species and roasting degree: the correlation of acrylamide with asparagine and free sugars. Food Sci Biotechnol 2024; 33:2333-2342. [PMID: 39145120 PMCID: PMC11319545 DOI: 10.1007/s10068-024-01633-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 08/16/2024] Open
Abstract
Acrylamide is a well-recognized hazardous compound with known carcinogenic, genotoxic, neurotoxic, and reproductive toxic effects. This research aimed to investigate how different legume species and roasting durations influence acrylamide formation during air-fryer roasting. The study also examined the relationship between acrylamide formation and the levels of free asparagine and free sugars in different bean species. Asparagine content varies substantially across different bean species. Sucrose was the predominant sugar across all bean species, with smaller amounts of galactose and glucose. Air-fryer-roasted Wandu kong (garden pea) showed the highest acrylamide formation, followed by Ultari kong (kidney bean) and Heoktae (black soybean), in that order. Beans roasted for longer periods in an air fryer contained significantly higher levels of acrylamide. This study revealed a strong positive correlation between acrylamide formation and the level of free asparagine in the beans, highlighting the risks associated with certain legume species and air-fryer roasting durations.
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Affiliation(s)
- Mun Yhung Jung
- College of Food Science, Woosuk University, Samnye, Wanju, Jeonbuk Province 55338 Republic of Korea
| | - Chung Hun Baek
- College of Food Science, Woosuk University, Samnye, Wanju, Jeonbuk Province 55338 Republic of Korea
| | - Yongzhe Ma
- College of Food Science, Woosuk University, Samnye, Wanju, Jeonbuk Province 55338 Republic of Korea
| | - Hee Won Lee
- College of Food Science, Woosuk University, Samnye, Wanju, Jeonbuk Province 55338 Republic of Korea
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3
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Jurado M, García-Fernández C, Campa A, Ferreira JJ. Identification of consistent QTL and candidate genes associated with seed traits in common bean by combining GWAS and RNA-Seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:143. [PMID: 38801535 PMCID: PMC11130024 DOI: 10.1007/s00122-024-04638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
KEY MESSAGE Association analysis, colocation study with previously reported QTL, and differential expression analyses allowed the identification of the consistent QTLs and main candidate genes controlling seed traits. Common beans show wide seed variations in shape, size, water uptake, and coat proportion. This study aimed to identify consistent genomic regions and candidate genes involved in the genetic control of seed traits by combining association and differential expression analyses. In total, 298 lines from the Spanish Diversity Panel were genotyped with 4,658 SNP and phenotyped for seven seed traits in three seasons. Thirty-eight significant SNP-trait associations were detected, which were grouped into 23 QTL genomic regions with 1,605 predicted genes. The positions of the five QTL regions associated with seed weight were consistent with previously reported QTL. HCPC analysis using the SNP that tagged these five QTL regions revealed three main clusters with significantly different seed weights. This analysis also separated groups that corresponded well with the two gene pools described: Andean and Mesoamerican. Expression analysis was performed on the seeds of the cultivar 'Xana' in three seed development stages, and 1,992 differentially expressed genes (DEGs) were detected, mainly when comparing the early and late seed development stages (1,934 DEGs). Overall, 91 DEGs related to cell growth, signaling pathways, and transcriptomic factors underlying these 23 QTL were identified. Twenty-two DEGs were located in the five QTL regions associated with seed weight, suggesting that they are the main set of candidate genes controlling this character. The results confirmed that seed weight is the sum of the effects of a complex network of loci, and contributed to the understanding of seed phenotype control.
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Affiliation(s)
- Maria Jurado
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Carmen García-Fernández
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Ana Campa
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Juan Jose Ferreira
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain.
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4
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Sá AGA, House JD. Adding pulse flours to cereal-based snacks and bakery products: An overview of free asparagine quantification methods and mitigation strategies of acrylamide formation in foods. Compr Rev Food Sci Food Saf 2024; 23:e13260. [PMID: 38284574 DOI: 10.1111/1541-4337.13260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024]
Abstract
Thermal processing techniques can lead to the formation of heat-induced toxic substances. Acrylamide is one contaminant that has received much scientific attention in recent years, and it is formed essentially during the Maillard reaction when foods rich in carbohydrates, particularly reducing sugars (glucose, fructose), and certain free amino acids, especially asparagine (ASN), are processed at high temperatures (>120°C). The highly variable free ASN concentration in raw materials makes it challenging for food businesses to keep acrylamide content below the European Commission benchmark levels, while avoiding flavor, color, and texture impacts on their products. Free ASN concentrations in crops are affected by environment, genotype, and soil fertilization, which can also influence protein content and amino acid composition. This review aims to provide an overview of free ASN and acrylamide quantification methods and mitigation strategies for acrylamide formation in foods, focusing on adding pulse flours to cereal-based snacks and bakery products. Overall, this review emphasizes the importance of these mitigation strategies in minimizing acrylamide formation in plant-based products and ensuring safer and healthier food options.
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Affiliation(s)
- Amanda G A Sá
- Richardson Centre for Food Technology and Research, Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James D House
- Richardson Centre for Food Technology and Research, Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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5
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Park HR, Seo JH, Kang BK, Kim JH, Heo SV, Choi MS, Ko JY, Kim CS. QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean. PLANTS (BASEL, SWITZERLAND) 2023; 12:3589. [PMID: 37896053 PMCID: PMC10610525 DOI: 10.3390/plants12203589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
This study aimed to discover the quantitative trait loci (QTL) associated with a high seed protein content in soybean and unravel the potential candidate genes. We developed two recombinant inbred line populations: YS and SI, by crossing Saedanbaek (high protein) with YS2035-B-91-1-B-1 (low protein) and Saedanbaek with Ilmi (low protein), respectively, and evaluated the protein content for three consecutive years. Using single-nucleotide polymorphism (SNP)-marker-based linkage maps, four QTLs were located on chromosomes 15, 18, and 20 with high logarithm of odds values (5.9-55.0), contributing 5.5-66.0% phenotypic variance. In all three experimental years, qPSD20-1 and qPSD20-2 were stable and identified in overlapping positions in the YS and SI populations, respectively. Additionally, novel QTLs were identified on chromosomes 15 and 18. Considering the allelic sequence variation between parental lines, 28 annotated genes related to soybean seed protein-including starch, lipid, and fatty acid biosynthesis-related genes-were identified within the QTL regions. These genes could potentially affect protein accumulation during seed development, as well as sucrose and oil metabolism. Overall, this study offers insights into the genetic mechanisms underlying a high soybean protein content. The identified potential candidate genes can aid marker-assisted selection for developing soybean lines with an increased protein content.
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Affiliation(s)
| | - Jeong Hyun Seo
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea; (H.R.P.); (B.K.K.); (J.H.K.); (S.V.H.); (M.S.C.); (J.Y.K.); (C.S.K.)
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6
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Pavlovic T, Margarit E, Müller GL, Saenz E, Ruzzo AI, Drincovich MF, Borrás L, Saigo M, Wheeler MCG. Differential metabolic reprogramming in developing soybean embryos in response to nutritional conditions and abscisic acid. PLANT MOLECULAR BIOLOGY 2023; 113:89-103. [PMID: 37702897 DOI: 10.1007/s11103-023-01377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Seed storage compound deposition is influenced by both maternal and filial tissues. Within this framework, we analyzed strategies that operate during the development and filling of soybean embryos, using in vitro culture systems combined with metabolomics and proteomics approaches. The carbon:nitrogen ratio (C:N) of the maternal supply and the hormone abscisic acid (ABA) are specific and interacting signals inducing differential metabolic reprogrammings linked to changes in the accumulation of storage macromolecules like proteins or oils. Differences in the abundance of sugars, amino acids, enzymes, transporters, transcription factors, and proteins involved in signaling were detected. Embryos adapted to the nutritional status by enhancing the metabolism of both carbon and nitrogen under lower C:N ratio condition or only carbon under higher C:N ratio condition. ABA turned off multiple pathways especially in high availability of amino acids, prioritizing the storage compounds biosynthesis. Common responses induced by ABA involved increased sucrose uptake (to increase the sink force) and oleosin (oil body structural component) accumulation. In turn, ABA differentially promoted protein degradation under lower nitrogen supply in order to sustain the metabolic demands. Further, the operation of a citrate shuttle was suggested by transcript quantification and enzymatic activity measurements. The results obtained are useful to help define biotechnological tools and technological approaches to improve oil and protein yields, with direct impact on human and animal nutrition as well as in green chemistry.
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Affiliation(s)
- Tatiana Pavlovic
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Gabriela Leticia Müller
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Ezequiel Saenz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino CC14, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Andrés Iván Ruzzo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - María Fabiana Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina
| | - Lucas Borrás
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino CC14, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Mariana Saigo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina.
| | - Mariel Claudia Gerrard Wheeler
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, S2000LRJ, Rosario, Santa Fe, Argentina.
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7
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Hooker JC, Smith M, Zapata G, Charette M, Luckert D, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Lefebvre F, Golshani A, Cober ER, Samanfar B. Differential gene expression provides leads to environmentally regulated soybean seed protein content. FRONTIERS IN PLANT SCIENCE 2023; 14:1260393. [PMID: 37790790 PMCID: PMC10544915 DOI: 10.3389/fpls.2023.1260393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023]
Abstract
Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans.
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Affiliation(s)
- Julia C. Hooker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Myron Smith
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Martin Charette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doris Luckert
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Ramona M. Mohr
- Brandon Research Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Mehri Hadinezhad
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | | | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Elroy R. Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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8
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Liu S, Liu Z, Hou X, Li X. Genetic mapping and functional genomics of soybean seed protein. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:29. [PMID: 37313523 PMCID: PMC10248706 DOI: 10.1007/s11032-023-01373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01373-5.
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Affiliation(s)
- Shu Liu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhaojun Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
| | - Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
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9
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Diers BW, Specht JE, Graef GL, Song Q, Rainey KM, Ramasubramanian V, Liu X, Myers CL, Stupar RM, An YQC, Beavis WD. Genetic architecture of protein and oil content in soybean seed and meal. THE PLANT GENOME 2023; 16:e20308. [PMID: 36744727 DOI: 10.1002/tpg2.20308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/09/2023] [Indexed: 05/10/2023]
Abstract
Soybean is grown primarily for the protein and oil extracted from its seed and its value is influenced by these components. The objective of this study was to map marker-trait associations (MTAs) for the concentration of seed protein, oil, and meal protein using the soybean nested association mapping (SoyNAM) population. The composition traits were evaluated on seed harvested from over 5000 inbred lines of the SoyNAM population grown in 10 field locations across 3 years. Estimated heritabilities were at least 0.85 for all three traits. The genotyping of lines with single nucleotide polymorphism markers resulted in the identification of 107 MTAs for the three traits. When MTAs for the three traits that mapped within 5 cM intervals were binned together, the MTAs were mapped to 64 intervals on 19 of the 20 soybean chromosomes. The majority of the MTA effects were small and of the 107 MTAs, 37 were for protein content, 39 for meal protein, and 31 for oil content. For cases where a protein and oil MTAs mapped to the same interval, most (94%) significant effects were opposite for the two traits, consistent with the negative correlation between these traits. A coexpression analysis identified candidate genes linked to MTAs and 18 candidate genes were identified. The large number of small effect MTAs for the composition traits suggest that genomic prediction would be more effective in improving these traits than marker-assisted selection.
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Affiliation(s)
- Brian W Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - James E Specht
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | - George L Graef
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | | | - Xiaotong Liu
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Yong-Qiang Charles An
- USDA-ARS Plant Genetic Research Unit at Donald Danforth Plant Science Center, St. Louis, MO, USA
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10
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Pajak A, Zaman D, Ajewole E, Pandurangan S, Marsolais F. Diurnal accumulation of K +-dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.). PHYTOCHEMISTRY 2023; 205:113489. [PMID: 36328196 DOI: 10.1016/j.phytochem.2022.113489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/23/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
L-Asparaginase (EC 3.5.1.1) activity has been previously reported to fluctuate with the photoperiod in young pea leaves, with higher activity in the light. The present research sought to investigate this phenomenon in developing leaves of common bean (Phaseolus vulgaris L.). There are two genes coding for K+-dependent asparaginase in this species. Expression of PvASPG1 predominates over PvASPG2 in all tissues. The catalytic efficiency of recombinant PvASPG2 was approximately 2-fold lower than that of PvASPG1. Polyclonal antibodies were raised against a specific peptide present in PvASPG1 to use in immunoblotting. In developing seed, asparaginase protein levels in the seed coat stayed constant, whereas levels in cotyledon were lower and progressively declined. In young leaf, asparagine protein levels showed diurnal variation, increasing at the end of the dark period and slowly decreasing during the light period. This was paralleled by changes in activity levels in leaf extracts. These changes accompanied a transient increase in free asparagine concentration at the beginning of the light period. The present results demonstrated that K+-dependent asparaginase activity reaches a maximum level at the transition from dark to light, anticipating dawn, in young leaves of common bean.
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Affiliation(s)
- Aga Pajak
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada.
| | - Dristy Zaman
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada; Department of Biology, University of Western Ontario, 1151 Richmond St., London, Ontario, N6A 5B7, Canada.
| | - Ebenezer Ajewole
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada; Department of Biology, University of Western Ontario, 1151 Richmond St., London, Ontario, N6A 5B7, Canada.
| | - Sudhakar Pandurangan
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada.
| | - Frédéric Marsolais
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada; Department of Biology, University of Western Ontario, 1151 Richmond St., London, Ontario, N6A 5B7, Canada.
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11
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Lou H, Yang Y, Zheng S, Ma Z, Chen W, Yu C, Song L, Wu J. Identification of key genes contributing to amino acid biosynthesis in Torreya grandis using transcriptome and metabolome analysis. Food Chem 2022; 379:132078. [PMID: 35063846 DOI: 10.1016/j.foodchem.2022.132078] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
Abstract
Torreya grandis has high economic and nutritional value due to the high nutrients in its kernels. The kernels of different development stages vary enormously in their amino acids content. However, the molecular basis and the regulatory mechanism of amino acid biosynthesis remain unclear. Here, transcriptome and metabolome analysis were performed. Correlation analysis result showed that 4 unigenes were significantly and positively correlated with at least 10 amino acids. The full length CDS of 2 unigenes (TgDAHP2 and TgASA1) were successfully cloned from the 4 unigenes for DAHP, ASA and CITS. Subcelluar localization analysis showed that both TgDAHP2 and TgASA1 were localized to the chloroplast. Overexpression of TgDAHP2 and TgASA1 in Arabidopsis can greatly increase the content of most amino acids. Moreover, 3 transcription factors were found to positively regulate the expression of TgASA1. This research contributes to understand the molecular regulatory mechanisms of amino acid biosynthesis in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yi Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhenmin Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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12
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Shrestha V, Yobi A, Slaten ML, Chan YO, Holden S, Gyawali A, Flint-Garcia S, Lipka AE, Angelovici R. Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition. PLANT PHYSIOLOGY 2022; 188:111-133. [PMID: 34618082 PMCID: PMC8774818 DOI: 10.1093/plphys/kiab390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
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Affiliation(s)
- Vivek Shrestha
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Marianne L Slaten
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Yen On Chan
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Samuel Holden
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abiskar Gyawali
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
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13
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Qin J, Wang F, Zhao Q, Shi A, Zhao T, Song Q, Ravelombola W, An H, Yan L, Yang C, Zhang M. Identification of Candidate Genes and Genomic Selection for Seed Protein in Soybean Breeding Pipeline. FRONTIERS IN PLANT SCIENCE 2022; 13:882732. [PMID: 35783963 PMCID: PMC9244705 DOI: 10.3389/fpls.2022.882732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/16/2022] [Indexed: 05/13/2023]
Abstract
Soybean is a primary meal protein for human consumption, poultry, and livestock feed. In this study, quantitative trait locus (QTL) controlling protein content was explored via genome-wide association studies (GWAS) and linkage mapping approaches based on 284 soybean accessions and 180 recombinant inbred lines (RILs), respectively, which were evaluated for protein content for 4 years. A total of 22 single nucleotide polymorphisms (SNPs) associated with protein content were detected using mixed linear model (MLM) and general linear model (GLM) methods in Tassel and 5 QTLs using Bayesian interval mapping (IM), single-trait multiple interval mapping (SMIM), single-trait composite interval mapping maximum likelihood estimation (SMLE), and single marker regression (SMR) models in Q-Gene and IciMapping. Major QTLs were detected on chromosomes 6 and 20 in both populations. The new QTL genomic region on chromosome 6 (Chr6_18844283-19315351) included 7 candidate genes and the Hap.X AA at the Chr6_19172961 position was associated with high protein content. Genomic selection (GS) of protein content was performed using Bayesian Lasso (BL) and ridge regression best linear unbiased prediction (rrBULP) based on all the SNPs and the SNPs significantly associated with protein content resulted from GWAS. The results showed that BL and rrBLUP performed similarly; GS accuracy was dependent on the SNP set and training population size. GS efficiency was higher for the SNPs derived from GWAS than random SNPs and reached a plateau when the number of markers was >2,000. The SNP markers identified in this study and other information were essential in establishing an efficient marker-assisted selection (MAS) and GS pipelines for improving soybean protein content.
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Affiliation(s)
- Jun Qin
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Fengmin Wang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Qingsong Zhao
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
- *Correspondence: Ainong Shi,
| | - Tiantian Zhao
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Qijian Song
- Soybean Genomics and Improvement Lab, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Waltram Ravelombola
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Hongzhou An
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Long Yan
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Chunyan Yang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Chunyan Yang,
| | - Mengchen Zhang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Hebei Laboratory of Crop Genetics and Breeding, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Mengchen Zhang,
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14
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Li X, Wang P, Zhang K, Liu S, Qi Z, Fang Y, Wang Y, Tian X, Song J, Wang J, Yang C, Sun X, Tian Z, Li WX, Ning H. Fine mapping QTL and mining genes for protein content in soybean by the combination of linkage and association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1095-1122. [PMID: 33420806 DOI: 10.1007/s00122-020-03756-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 12/19/2020] [Indexed: 05/29/2023]
Abstract
Soybean is one main source of dietary protein; therefore, improving protein content is an important objective in breeding programs. There is a significant negative correlation between protein and oil content, which influenced mapping quantitative trait locus (QTL) and quantitative trait nucleotides for these two traits. In this study, a linkage map was created with 2232 single-nucleotide polymorphism markers for the four-way recombinant inbred line (FW-RIL) population derived from the cross (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19), and then conditional and unconditional QTL analyses were carried out by inclusive complete interval mapping based on the phenotypic data of protein and oil content collected in 10 different environments. As shown in the results of linkage analysis, a total of 85 QTL have been detected. We have performed association analysis using 109,676 markers after quality filtering for FW-RIL, and the results have shown that a total of 60 QTNs were detected. We have performed association analysis using 63,306 markers after quality filtering for resource population, and the results have shown that a total of 123 QTNs were detected. We have combined linkage and association analysis, and there are six QTNs verified by FW-RIL and resource population. We have performed pathway analysis on the genes in these six QTN attenuation regions, and the result shows that a total of four candidate genes are related to the synthesis or metabolism of soybean protein. These findings will facilitate marker-assisted selection and molecular breeding of soybean.
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Affiliation(s)
- Xiyu Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Ping Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
- Huaiyin Institute of Technology, Huaian, China
| | - Kaixin Zhang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhongying Qi
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Yanlong Fang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaocui Tian
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Jie Song
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Jiajing Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chang Yang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Xu Sun
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
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15
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The SV, Snyder R, Tegeder M. Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency. FRONTIERS IN PLANT SCIENCE 2021; 11:628366. [PMID: 33732269 PMCID: PMC7957077 DOI: 10.3389/fpls.2020.628366] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/31/2020] [Indexed: 05/22/2023]
Abstract
In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.
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Affiliation(s)
| | | | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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16
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Lee S, Park J, Lee J, Shin D, Marmagne A, Lim PO, Masclaux-Daubresse C, An G, Nam HG. OsASN1 Overexpression in Rice Increases Grain Protein Content and Yield under Nitrogen-Limiting Conditions. PLANT & CELL PHYSIOLOGY 2020; 61:1309-1320. [PMID: 32384162 PMCID: PMC7377344 DOI: 10.1093/pcp/pcaa060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/28/2020] [Indexed: 05/10/2023]
Abstract
Nitrogen (N) is a major limiting factor affecting crop yield in unfertilized soil. Thus, cultivars with a high N use efficiency (NUE) and good grain protein content (GPC) are needed to fulfill the growing food demand and to reduce environmental burden. This is especially true for rice (Oryza sativa L.) that is cultivated with a high input of N fertilizer and is a primary staple food crop for more than half of the global population. Here, we report that rice asparagine synthetase 1 (OsASN1) is required for grain yield and grain protein contents under both N-sufficient (conventional paddy fields) and N-limiting conditions from analyses of knockout mutant plants. In addition, we show that overexpression (OX) of OsASN1 results in better nitrogen uptake and assimilation, and increased tolerance to N limitation at the seedling stage. Under field conditions, the OsASN1 OX rice plants produced grains with increased N and protein contents without yield reduction compared to wild-type (WT) rice. Under N-limited conditions, the OX plants displayed increased grain yield and protein content with enhanced photosynthetic activity compared to WT rice. Thus, OsASN1 can be an effective target gene for the development of rice cultivars with higher grain protein content, NUE, and grain yield under N-limiting conditions.
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Affiliation(s)
- Sichul Lee
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Korea
| | - Joonheum Park
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Korea
| | - Jinwon Lee
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Korea
| | - Dongjin Shin
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Korea
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Pyung Ok Lim
- Department of New Biology, DGIST, Daegu 42988, Korea
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Gynheung An
- Department of Genetic Engineering and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
- Corresponding authors: Gynheung An, E-mail, ; Fax, +82312034969; Hong Gil Nam, E-mail, ; Fax, +82537851859
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Korea
- Department of New Biology, DGIST, Daegu 42988, Korea
- Corresponding authors: Gynheung An, E-mail, ; Fax, +82312034969; Hong Gil Nam, E-mail, ; Fax, +82537851859
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17
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Min CW, Park J, Bae JW, Agrawal GK, Rakwal R, Kim Y, Yang P, Kim ST, Gupta R. In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells 2020; 9:E1517. [PMID: 32580392 PMCID: PMC7349688 DOI: 10.3390/cells9061517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Jin Woo Bae
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea;
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265, Kathmandu 44600, Nepal; (G.K.A.); (R.R.)
- GRADE (Global Research Arch for Developing Education) Academy Private Limited, Adarsh Nagar-13, Birgunj 44300, Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1Tennodai, Tsukuba 3058574, Japan
| | - Youngsoo Kim
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, Seoul 03080, Korea; (J.P.); (Y.K.)
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
| | - Ravi Gupta
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Korea;
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
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18
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Bonnot T, Martre P, Hatte V, Dardevet M, Leroy P, Bénard C, Falagán N, Martin-Magniette ML, Deborde C, Moing A, Gibon Y, Pailloux M, Bancel E, Ravel C. Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency. PLANT PHYSIOLOGY 2020; 183:501-516. [PMID: 32295821 PMCID: PMC7271774 DOI: 10.1104/pp.19.00842] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/27/2020] [Indexed: 05/06/2023]
Abstract
Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.
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Affiliation(s)
- Titouan Bonnot
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Pierre Martre
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Victor Hatte
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Mireille Dardevet
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Philippe Leroy
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Camille Bénard
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Natalia Falagán
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie-Laure Martin-Magniette
- L'Institut des Sciences des Plantes (IPS2), CNRS, INRAE, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91400 Orsay, France
- Mathématiques et informatique appliqués (MIA)-Paris, AgroParisTech, INRAE, Université Paris-Saclay, 75231 Paris, France
| | - Catherine Deborde
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Annick Moing
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Yves Gibon
- Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, Plateforme Métabolome Bordeaux, MetaboHUB-PHENOME, 33140 Villenave d'Ornon, France
| | - Marie Pailloux
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Centre National de la Recherche Scientifique (CNRS), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Emmanuelle Bancel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | - Catherine Ravel
- Genetics Diversity and Ecophysiology of Cereals, Institut National de l'Agriculture, de l'Alimentation et de l'Environnement (INRAE), Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
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19
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Joshi J, Renaud JB, Sumarah MW, Marsolais F. Deciphering S-methylcysteine biosynthesis in common bean by isotopic tracking with mass spectrometry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:176-186. [PMID: 31215701 DOI: 10.1111/tpj.14438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/22/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The suboptimal content of sulfur-containing amino acids methionine and cysteine prevents common bean (Phaseolus vulgaris) from being an excellent source of protein. Nutritional improvements to this significant crop require a better understanding of the biosynthesis of sulfur-containing compounds including the nonproteogenic amino acid S-methylcysteine and the dipeptide γ-glutamyl-S-methylcysteine, which accumulate in seed. In this study, seeds were incubated with isotopically labelled serine, cysteine or methionine and analyzed by reverse phase chromatography-high resolution mass spectrometry to track stable isotopes as they progressed through the sulfur metabolome. We determined that serine and methionine are the sole precursors of free S-methylcysteine in developing seeds, indicating that this compound is likely to be synthesized through the condensation of O-acetylserine and methanethiol. BSAS4;1, a cytosolic β-substituted alanine synthase preferentially expressed in developing seeds, catalyzed the formation of S-methylcysteine in vitro. A higher flux of labelled serine or cysteine was observed in a sequential pathway involving γ-glutamyl-cysteine, homoglutathione and S-methylhomoglutathione, a likely precursor to γ-glutamyl-S-methylcysteine. Preferential incorporation of serine over cysteine supports a subcellular compartmentation of this pathway, likely to be in the chloroplast. The origin of the methyl group in S-methylhomoglutathione was traced to methionine. There was substantial incorporation of carbons from methionine into the β-alanine portion of homoglutathione and S-methylhomoglutathione, suggesting the breakdown of methionine by methionine γ-lyase and conversion of α-ketobutyrate to β-alanine via propanoate metabolism. These findings delineate the biosynthetic pathways of the sulfur metabolome of common bean and provide an insight that will aid future efforts to improve nutritional quality.
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Affiliation(s)
- Jaya Joshi
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario, N6A 3K7, Canada
| | - Justin B Renaud
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Mark W Sumarah
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Frédéric Marsolais
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario, N6A 3K7, Canada
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20
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Wang J, Zhou P, Shi X, Yang N, Yan L, Zhao Q, Yang C, Guan Y. Primary metabolite contents are correlated with seed protein and oil traits in near-isogenic lines of soybean. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Li S, Xu H, Yang J, Zhao T. Dissecting the Genetic Architecture of Seed Protein and Oil Content in Soybean from the Yangtze and Huaihe River Valleys Using Multi-Locus Genome-Wide Association Studies. Int J Mol Sci 2019; 20:E3041. [PMID: 31234445 PMCID: PMC6628128 DOI: 10.3390/ijms20123041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/19/2022] Open
Abstract
Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein and oil content are two valuable quality traits controlled by multiple genes in soybean. In this study, the restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) procedure was performed to dissect the genetic architecture of seed protein and oil content in a diverse panel of 279 soybean accessions from the Yangtze and Huaihe River Valleys in China. We identified 26 quantitative trait loci (QTLs) for seed protein content and 23 for seed oil content, including five associated with both traits. Among these, 39 QTLs corresponded to previously reported QTLs, whereas 10 loci were novel. As reported previously, the QTL on chromosome 20 was associated with both seed protein and oil content. This QTL exhibited opposing effects on these traits and contributed the most to phenotype variation. From the detected QTLs, 55 and 51 candidate genes were identified for seed protein and oil content, respectively. Among these genes, eight may be promising candidate genes for improving soybean nutritional quality. These results will facilitate marker-assisted selective breeding for soybean protein and oil content traits.
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Affiliation(s)
- Shuguang Li
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu/Huai'an Key Laboratory for Agricultural Biotechnology, Huai'an 223001, China.
| | - Haifeng Xu
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu/Huai'an Key Laboratory for Agricultural Biotechnology, Huai'an 223001, China.
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu/Huai'an Key Laboratory for Agricultural Biotechnology, Huai'an 223001, China.
| | - Tuanjie Zhao
- Soybean research institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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22
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Shariati S, Zare D, Mirdamadi S. Screening of carbon and nitrogen sources using mixture analysis designs for carotenoid production by Blakeslea trispora. Food Sci Biotechnol 2019; 28:469-479. [PMID: 30956859 PMCID: PMC6431355 DOI: 10.1007/s10068-018-0484-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/26/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
The production of many secondary metabolites such as carotenoids is influenced by the type of carbon and nitrogen sources and C:N ratio applied in culture medium. The present study discusses the role of C:N ratio and screening of carbon and nitrogen sources using mixture analysis design in carotenoids production by Blakeslea trispora. The C:N ratios of 20, 40, and 60 with six nitrogen sources were evaluated. Results indicated that limitation of nitrogen source (C:N of 60) could improve carotenoids production. Six nitrogen and carbon sources were then screened using mixture analysis design. The most effective nitrogen and carbon sources were soybean powder and glucose, respectively. The productivity of carotenoids (983.8 ± 31.5 mg/L) based on consumed nitrogen and carbon source was 189.10 mg/g soybean powder and 19.66 mg/g glucose. Mixture analysis design indicated single carbon and nitrogen source were more effective than a mixture of sources for carotenoids production.
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Affiliation(s)
- Sepideh Shariati
- Pharmaceutical Sciences Branch, Islamic Azad University, 1941933111 Tehran, Islamic Republic of Iran
| | - Davood Zare
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
| | - Saeed Mirdamadi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
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23
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Su D, Jiang S, Wang J, Yang C, Li W, Li WX, Ning H. Identification of major QTLs associated with agronomical traits and candidate gene mining in soybean. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1674691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Daiqun Su
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Sitong Jiang
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Jiajing Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Chang Yang
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Wenbin Li
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Harbin, PR China
- Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Harbin, PR China
- Department Agronomy Soybean Research Institute, Northeast Agricultural University, Harbin, PR China
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24
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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25
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Qi Z, Zhang Z, Wang Z, Yu J, Qin H, Mao X, Jiang H, Xin D, Yin Z, Zhu R, Liu C, Yu W, Hu Z, Wu X, Liu J, Chen Q. Meta-analysis and transcriptome profiling reveal hub genes for soybean seed storage composition during seed development. PLANT, CELL & ENVIRONMENT 2018; 41:2109-2127. [PMID: 29486529 DOI: 10.1111/pce.13175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Soybean is an important crop providing edible oil and protein source. Soybean oil and protein contents are quantitatively inherited and significantly affected by environmental factors. In this study, meta-analysis was conducted based on soybean physical maps to integrate quantitative trait loci (QTLs) from multiple experiments in different environments. Meta-QTLs for seed oil, fatty acid composition, and protein were identified. Of them, 11 meta-QTLs were located on hot regions for both seed oil and protein. Next, we selected 4 chromosome segment substitution lines with different seed oil and protein contents to characterize their 3 years of phenotype selection in the field. Using strand-specific RNA-sequencing analysis, we profile the time-course transcriptome patterns of soybean seeds at early maturity, middle maturity, and dry seed stages. Pairwise comparison and K-means clustering analysis revealed 7,482 differentially expressed genes and 45 expression patterns clusters. Weighted gene coexpression network analysis uncovered 46 modules of gene expression patterns. The 2 most significant coexpression networks were visualized, and 7 hub genes were identified that were involved in soybean oil and seed storage protein accumulation processes. Our results provided a transcriptome dataset for soybean seed development, and the candidate hub genes represent a foundation for further research.
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Affiliation(s)
- Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhongyu Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingyao Yu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongtao Qin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xinrui Mao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhengong Yin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Rongsheng Zhu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Wei Yu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
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26
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Ajewole E, Santamaria‐Kisiel L, Pajak A, Jaskolski M, Marsolais F. Structural basis of potassium activation in plant asparaginases. FEBS J 2018; 285:1528-1539. [DOI: 10.1111/febs.14428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/07/2018] [Accepted: 02/27/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Ebenezer Ajewole
- Department of Biology University of Western Ontario London Canada
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
| | | | - Agnieszka Pajak
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
- Department of Crystallography Faculty of Chemistry A. Mickiewicz University Poznan Poland
| | - Frédéric Marsolais
- Department of Biology University of Western Ontario London Canada
- London Research and Development Centre Agriculture and Agri‐Food Canada London Canada
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27
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Gaufichon L, Marmagne A, Belcram K, Yoneyama T, Sakakibara Y, Hase T, Grandjean O, Clément G, Citerne S, Boutet-Mercey S, Masclaux-Daubresse C, Chardon F, Soulay F, Xu X, Trassaert M, Shakiebaei M, Najihi A, Suzuki A. ASN1-encoded asparagine synthetase in floral organs contributes to nitrogen filling in Arabidopsis seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:371-393. [PMID: 28390103 DOI: 10.1111/tpj.13567] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 03/20/2017] [Accepted: 03/28/2017] [Indexed: 05/23/2023]
Abstract
Despite a general view that asparagine synthetase generates asparagine as an amino acid for long-distance transport of nitrogen to sink organs, its role in nitrogen metabolic pathways in floral organs during seed nitrogen filling has remained undefined. We demonstrate that the onset of pollination in Arabidopsis induces selected genes for asparagine metabolism, namely ASN1 (At3g47340), GLN2 (At5g35630), GLU1 (At5g04140), AapAT2 (At5g19950), ASPGA1 (At5g08100) and ASPGB1 (At3g16150), particularly at the ovule stage (stage 0), accompanied by enhanced asparagine synthetase protein, asparagine and total amino acids. Immunolocalization confined asparagine synthetase to the vascular cells of the silique cell wall and septum, but also to the outer and inner seed integuments, demonstrating the post-phloem transport of asparagine in these cells to developing embryos. In the asn1 mutant, aberrant embryo cell divisions in upper suspensor cell layers from globular to heart stages assign a role for nitrogen in differentiating embryos within the ovary. Induction of asparagine metabolic genes by light/dark and nitrate supports fine shifts of nitrogen metabolic pathways. In transgenic Arabidopsis expressing promoterCaMV35S ::ASN1 fusion, marked metabolomics changes at stage 0, including a several-fold increase in free asparagine, are correlated to enhanced seed nitrogen. However, specific promoterNapin2S ::ASN1 expression during seed formation and a six-fold increase in asparagine toward the desiccation stage result in wild-type seed nitrogen, underlining that delayed accumulation of asparagine impairs the timing of its use by releasing amide and amino nitrogen. Transcript and metabolite profiles in floral organs match the carbon and nitrogen partitioning to generate energy via the tricarboxylic acid cycle, GABA shunt and phosphorylated serine synthetic pathway.
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Affiliation(s)
- Laure Gaufichon
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Anne Marmagne
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Katia Belcram
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Observatoire du Végétal - Cytologie Imagerie, RD10, Versailles, F-78026, France
| | - Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, The University of Tokyo, Yayoi l-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yukiko Sakakibara
- Institute for Protein Research, Division of Protein Chemistry, Laboratory of Regulation of Biological Reactions, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshiharu Hase
- Institute for Protein Research, Division of Protein Chemistry, Laboratory of Regulation of Biological Reactions, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Olivier Grandjean
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Observatoire du Végétal - Cytologie Imagerie, RD10, Versailles, F-78026, France
| | - Gilles Clément
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Observatoire du Végétal - Chimie Métabolisme, RD10, Versailles, F-78026, France
| | - Sylvie Citerne
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Observatoire du Végétal - Chimie Métabolisme, RD10, Versailles, F-78026, France
| | - Stéphanie Boutet-Mercey
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Observatoire du Végétal - Chimie Métabolisme, RD10, Versailles, F-78026, France
| | | | - Fabien Chardon
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Fabienne Soulay
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Xiaole Xu
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Marion Trassaert
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Maryam Shakiebaei
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Amina Najihi
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
| | - Akira Suzuki
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France
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28
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Combining Isotope Labelling with High Resolution Liquid Chromatography-Tandem Mass Spectrometry to Study Sulfur Amino Acid Metabolism in Seeds of Common Bean (Phaseolus vulgaris). ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-56526-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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29
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Taliercio E, Eickholt D, Rouf R, Carter T. Changes in gene expression between a soybean F1 hybrid and its parents are associated with agronomically valuable traits. PLoS One 2017; 12:e0177225. [PMID: 28493991 PMCID: PMC5426663 DOI: 10.1371/journal.pone.0177225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Soybean [Glycine max (L.) Merr.] genetic diversity is limited because domesticated soybean has undergone multiple genetic bottlenecks. Its progenitor, the wild soybean [Glycine soja Siebold & Zucc], has not undergone the same intense selection and is much more genetically diverse than domesticated soybean. However, the agronomic importance of diversity in wild soybean is unclear, and its weedy nature makes assessment difficult. To address this issue, we chose for study a highly selected, adapted F4-derived progeny of wild soybean, NMS4-44-329. This breeding line is derived from the hybridization between G. max cultivar N7103 and G. soja PI 366122. Agronomic comparisons were made among N7103, NMS4-44-329 and their F1 and F2 progeny in replicated yield trials at two North Carolina locations. Significant F1 mid-parent heterosis was observed at each location for seed yield (189 and 223 kgha-1, P<0.05 and P<0.10, respectively), seed protein content (1.1g/100g, P<0.01) and protein production per hectare (101 and 100 kgha-1, P<0.01 and P<0.06, respectively). Increased yield, seed protein content and protein production per hectare in the hybrids suggested that wild soybean has the potential to improve agronomic traits in applied breeding. Comparisons of differentially-expressed genes in the hybrid vs. parents identified genes associated with N metabolism. Non-additive changes in gene expression in the hybrids relative to the parents could reasonably explain the improved protein levels in the F1 hybrids. Changes in gene expression were influenced by environmental effects; however, allele specific bias in the hybrids were well correlated between environments. We propose that changes in gene expression, both additive and non-additive, and changes in allele specific expression bias may explain agronomic traits, and be valuable tools for plant breeders in the assessment of breeding populations.
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Affiliation(s)
- Earl Taliercio
- USDA-ARS, Raleigh, North Carolina United States of America
| | - David Eickholt
- Crop and Soil Science Department, North Carolina State University, Raleigh, NC, United States of America
| | - Rakin Rouf
- Crop and Soil Science Department, North Carolina State University, Raleigh, NC, United States of America
| | - Thomas Carter
- USDA-ARS, Raleigh, North Carolina United States of America
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30
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Huber SC, Li K, Nelson R, Ulanov A, DeMuro CM, Baxter I. Canopy position has a profound effect on soybean seed composition. PeerJ 2016; 4:e2452. [PMID: 27672507 PMCID: PMC5028787 DOI: 10.7717/peerj.2452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022] Open
Abstract
Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health in developing countries because food products produced from seeds at the bottom of the canopy contained higher Fe concentrations than products from the top of the canopy. Therefore, using seeds produced in the lower canopy for production of iron-rich soy foods for human consumption could be important when plants are the major source of protein and human diets can be chronically deficient in Fe and other minerals.
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Affiliation(s)
- Steven C Huber
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, Agricultural Research Service, Urbana, IL, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kunzhi Li
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, Agricultural Research Service, Urbana, IL, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Lab of Plant Nutrition Genetic Engineering, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Randall Nelson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Urbana, IL, United States
| | - Alexander Ulanov
- Metabolomics Facility, Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Catherine M DeMuro
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture, Agricultural Research Service, Urbana, IL, United States
| | - Ivan Baxter
- Plant Genetics Research Unit, United States Department of Agriculture Agricultural Research Service, St. Louis, MO, United States.,Donald Danforth Plant Science Center, Creve Coeur, MO, United States
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31
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Carter AM, Tegeder M. Increasing Nitrogen Fixation and Seed Development in Soybean Requires Complex Adjustments of Nodule Nitrogen Metabolism and Partitioning Processes. Curr Biol 2016; 26:2044-2051. [PMID: 27451897 DOI: 10.1016/j.cub.2016.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/19/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
Abstract
Legumes are able to access atmospheric di-nitrogen (N2) through a symbiotic relationship with rhizobia that reside within root nodules. In soybean, following N2 fixation by the bacteroids, ammonia is finally reduced in uninfected cells to allantoin and allantoic acid [1]. These ureides present the primary long-distance transport forms of nitrogen (N), and are exported from nodules via the xylem for shoot N supply. Transport of allantoin and allantoic acid out of nodules requires the function of ureide permeases (UPS1) located in cells adjacent to the vasculature [2, 3]. We expressed a common bean UPS1 transporter in cortex and endodermis cells of soybean nodules and found that delivery of N from nodules to shoot, as well as seed set, was significantly increased. In addition, the number of transgenic nodules was increased and symbiotic N2 fixation per nodule was elevated, indicating that transporter function in nodule N export is a limiting step in bacterial N acquisition. Further, the transgenic nodules showed considerable increases in nodule N assimilation, ureide synthesis, and metabolite levels. This suggests complex adjustments of nodule N metabolism and partitioning processes in support of symbiotic N2 fixation. We propose that the transgenic UPS1 plants display metabolic and allocation plasticity to overcome N2 fixation and seed yield limitations. Overall, it is demonstrated that transporter function in N export from nodules is a key step for enhancing atmospheric N2 fixation and nodule function and for improving shoot N nutrition and seed development in legumes.
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Affiliation(s)
- Amanda M Carter
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
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32
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Rao G, Sui J, Zhang J. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.). Biol Open 2016; 5:829-36. [PMID: 27215321 PMCID: PMC4920193 DOI: 10.1242/bio.017863] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r2≥0.49 and had a false discovery rate (FDR) ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism. Summary: This work provides a comprehensive metabolomic study of walnut kernels and reveals most of the carbohydrate and protein-derived carbons were transferred into other compounds during the maturation of walnuts.
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Affiliation(s)
- Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Republic of China Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
| | - Jinkai Sui
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Republic of China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Republic of China Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, Republic of China
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33
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Ma Y, Kan G, Zhang X, Wang Y, Zhang W, Du H, Yu D. Quantitative Trait Loci (QTL) Mapping for Glycinin and β-Conglycinin Contents in Soybean (Glycine max L. Merr.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3473-83. [PMID: 27070305 DOI: 10.1021/acs.jafc.6b00167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Compared to β-conglycinin, glycinin contains 3-4 times the methionine and cysteine (sulfur-containing amino acids), accounting for approximately 40 and 30%, respectively, of the total storage protein in soybean. Increasing the soybean storage protein content while improving the ratio of glycinin to β-conglycinin is of great significance for soybean breeding and soy food products. The objective of this study is to analyze the genetic mechanism regulating the glycinin and β-conglycinin contents of soybean by using a recombinant inbred line (RIL) population derived from a cross between Kefeng No. 1 and Nannong 1138-2. Two hundred and twenty-one markers were used to map quantitative trait loci (QTLs) for glycinin (11S) and β-conglycinin (7S) contents, the ratio of glycinin to β-conglycinin (RGC), and the sum of glycinin and β-conglycinin (SGC). A total of 35 QTLs, 3 pairs of epistatic QTLs, and 5 major regions encompassing multiple QTLs were detected. Genes encoding the subunits of β-conglycinin were localized to marker intervals sat_418-satt650 and sat_196-sat_303, which are linked to RGC and SGC; marker sat_318, associated with 11S, 7S, and SGC, was located near Glyma10g04280 (Gy4), which encodes a subunit of glycinin. These results, which take epistatic interactions into account, will improve our understanding of the genetic basis of 11S and 7S contents and will lay a foundation for marker-assisted selection (MAS) breeding of soybean and improving the quality of soybean products.
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Affiliation(s)
- Yujie Ma
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Xinnan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Yongli Wang
- Biofuels Institute, School of the Environment, Jiangsu University , Zhenjiang 212013, China
| | - Wei Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
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34
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Pandurangan S, Diapari M, Yin F, Munholland S, Perry GE, Chapman BP, Huang S, Sparvoli F, Bollini R, Crosby WL, Pauls KP, Marsolais F. Genomic Analysis of Storage Protein Deficiency in Genetically Related Lines of Common Bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2016; 7:389. [PMID: 27066039 PMCID: PMC4814446 DOI: 10.3389/fpls.2016.00389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/14/2016] [Indexed: 05/06/2023]
Abstract
A series of genetically related lines of common bean (Phaseolus vulgaris L.) integrate a progressive deficiency in major storage proteins, the 7S globulin phaseolin and lectins. SARC1 integrates a lectin-like protein, arcelin-1 from a wild common bean accession. SMARC1N-PN1 is deficient in major lectins, including erythroagglutinating phytohemagglutinin (PHA-E) but not α-amylase inhibitor, and incorporates also a deficiency in phaseolin. SMARC1-PN1 is intermediate and shares the phaseolin deficiency. Sanilac is the parental background. To understand the genomic basis for variations in protein profiles previously determined by proteomics, the genotypes were submitted to short-fragment genome sequencing using an Illumina HiSeq 2000/2500 platform. Reads were aligned to reference sequences and subjected to de novo assembly. The results of the analyses identified polymorphisms responsible for the lack of specific storage proteins, as well as those associated with large differences in storage protein expression. SMARC1N-PN1 lacks the lectin genes pha-E and lec4-B17, and has the pseudogene pdlec1 in place of the functional pha-L gene. While the α-phaseolin gene appears absent, an approximately 20-fold decrease in β-phaseolin accumulation is associated with a single nucleotide polymorphism converting a G-box to an ACGT motif in the proximal promoter. Among residual lectins compensating for storage protein deficiency, mannose lectin FRIL and α-amylase inhibitor 1 genes are uniquely present in SMARC1N-PN1. An approximately 50-fold increase in α-amylase inhibitor like protein accumulation is associated with multiple polymorphisms introducing up to eight potential positive cis-regulatory elements in the proximal promoter specific to SMARC1N-PN1. An approximately 7-fold increase in accumulation of 11S globulin legumin is not associated with variation in proximal promoter sequence, suggesting that the identity of individual proteins involved in proteome rebalancing might also be determined at the translational level.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Marwan Diapari
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Fuqiang Yin
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Seth Munholland
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - B. Patrick Chapman
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Shangzhi Huang
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Francesca Sparvoli
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - Roberto Bollini
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - William L. Crosby
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Karl P. Pauls
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- *Correspondence: Frédéric Marsolais,
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35
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Hettmer S, Schinzel AC, Tchessalova D, Schneider M, Parker CL, Bronson RT, Richards NG, Hahn WC, Wagers AJ. Functional genomic screening reveals asparagine dependence as a metabolic vulnerability in sarcoma. eLife 2015; 4. [PMID: 26499495 PMCID: PMC4695385 DOI: 10.7554/elife.09436] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/23/2015] [Indexed: 01/17/2023] Open
Abstract
Current therapies for sarcomas are often inadequate. This study sought to identify actionable gene targets by selective targeting of the molecular networks that support sarcoma cell proliferation. Silencing of asparagine synthetase (ASNS), an amidotransferase that converts aspartate into asparagine, produced the strongest inhibitory effect on sarcoma growth in a functional genomic screen of mouse sarcomas generated by oncogenic Kras and disruption of Cdkn2a. ASNS silencing in mouse and human sarcoma cell lines reduced the percentage of S phase cells and impeded new polypeptide synthesis. These effects of ASNS silencing were reversed by exogenous supplementation with asparagine. Also, asparagine depletion via the ASNS inhibitor amino sulfoximine 5 (AS5) or asparaginase inhibited mouse and human sarcoma growth in vitro, and genetic silencing of ASNS in mouse sarcoma cells combined with depletion of plasma asparagine inhibited tumor growth in vivo. Asparagine reliance of sarcoma cells may represent a metabolic vulnerability with potential anti-sarcoma therapeutic value. DOI:http://dx.doi.org/10.7554/eLife.09436.001 Sarcoma is a type of cancer that forms in the connective tissues of the body, such as bone, cartilage, muscle and fat. Usually, treatment involves surgical removal of the tumor and/or radiation to kill the tumor cells. However, if sarcomas spread to other parts of the body, the treatment options are limited. Genetic studies have revealed several genetic changes that contribute to the formation of sarcomas. Many sarcomas have a mutation in a gene that encodes a protein called Ras. In 2011, researchers found that injecting Ras mutant muscle cells into the muscles of mice could lead to the formation of sarcomas. Next, the researchers compared gene expression in the mouse sarcoma cells with gene expression in normal mouse muscle cells and found that certain genes appeared to be more highly expressed in the sarcoma cells. These genes were also hyperactive in human sarcoma cells and may promote the growth of sarcomas carrying mutant forms of Ras. Now, Hettmer et al. – including some of the same researchers involved in the earlier work – show that targeting one of these hyperactive genes can slow sarcoma growth. The experiments made use of a technique called ribonucleic acid interference (or RNAi for short) to specifically switch off the expression of the hyperactive genes and then observed how this affected sarcoma growth. Hettmer et al. found that blocking the expression of one particular gene, which encodes an enzyme called asparagine synthetase, slowed down the growth of the sarcoma the most. Asparagine synthetase makes the amino acid asparagine, which is needed to make proteins in cells. Further experiments showed that reducing the amount of asparagine in human and mouse sarcoma cells slowed down the growth of these cells. A drug that lowers the amount of asparagine in cells is already used to treat some blood cancers. Hettmer et al.’s findings suggest that drugs that alter the availability of asparagine in the body might also be useful to treat sarcomas with mutant forms of Ras. DOI:http://dx.doi.org/10.7554/eLife.09436.002
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Affiliation(s)
- Simone Hettmer
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, United States.,Pediatric Hematology/Oncology, Charité, University Hospital Berlin, Berlin, Germany.,Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany.,Joslin Diabetes Center, Harvard Medical School, Boston, United States
| | - Anna C Schinzel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Daria Tchessalova
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, United States.,Joslin Diabetes Center, Harvard Medical School, Boston, United States
| | - Michaela Schneider
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Christina L Parker
- Summer Honors Undergraduate Program, Harvard Medical School, Boston, United States.,University of Maryland, Baltimore County, Baltimore, United States
| | - Roderick T Bronson
- Department of Biomedical Sciences, Tufts University Veterinary School, North Grafton, United States
| | - Nigel Gj Richards
- Department of Chemistry and Chemical Biology, Indiana University - Purdue University Indianapolis, Indianapolis, United States
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, United States.,Joslin Diabetes Center, Harvard Medical School, Boston, United States
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36
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Pandurangan S, Pajak A, Rintoul T, Beyaert R, Hernández-Sebastià C, Brown DCW, Marsolais F. Soybean seeds overexpressing asparaginase exhibit reduced nitrogen concentration. PHYSIOLOGIA PLANTARUM 2015; 155:126-137. [PMID: 25898948 DOI: 10.1111/ppl.12341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 03/18/2015] [Accepted: 03/28/2015] [Indexed: 06/04/2023]
Abstract
In soybean seed, a correlation has been observed between the concentration of free asparagine at mid-maturation and protein concentration at maturity. In this study, a Phaseolus vulgaris K+ -dependent asparaginase cDNA, PvAspG2, was expressed in transgenic soybean under the control of the embryo specific promoter of the β-subunit of β-conglycinin. Three lines were isolated having high expression of the transgene at the transcript, protein and enzyme activity levels at mid-maturation, with a 20- to 40-fold higher asparaginase activity in embryo than a control line expressing β-glucuronidase. Increased asparaginase activity was associated with a reduction in free asparagine levels as a percentage of total free amino acids, by 11-18%, and an increase in free aspartic acid levels, by 25-60%. Two of the lines had reduced nitrogen concentration in mature seed as determined by nitrogen analysis, by 9-13%. Their levels of extractible globulins were reduced by 11-30%. This was accompanied by an increase in oil concentration, by 5-8%. The lack of change in nitrogen concentration in the third transgenic line was correlated with an increase in free glutamic acid levels by approximately 40% at mid-maturation.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Agnieszka Pajak
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Tara Rintoul
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Ronald Beyaert
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Cinta Hernández-Sebastià
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Daniel C W Brown
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
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37
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Pandurangan S, Sandercock M, Beyaert R, Conn KL, Hou A, Marsolais F. Differential response to sulfur nutrition of two common bean genotypes differing in storage protein composition. FRONTIERS IN PLANT SCIENCE 2015; 6:92. [PMID: 25750649 PMCID: PMC4335288 DOI: 10.3389/fpls.2015.00092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/04/2015] [Indexed: 05/28/2023]
Abstract
It has been hypothesized that the relatively low concentration of sulfur amino acids in legume seeds might be an ecological adaptation to nutrient poor, marginal soils. SARC1 and SMARC1N-PN1 are genetically related lines of common bean (dry bean, Phaseolus vulgaris) differing in seed storage protein composition. In SMARC1N-PN1, the lack of phaseolin and major lectins is compensated by increased levels of sulfur-rich proteins, resulting in an enhanced concentration of cysteine and methionine, mostly at the expense of the abundant non-protein amino acid, S-methylcysteine. To identify potential effects associated with an increased concentration of sulfur amino acids in the protein pool, the response of the two genotypes to low and high sulfur nutrition was evaluated under controlled conditions. Seed yield was increased by the high sulfate treatment in SMARC1N-PN1. The seed concentrations of sulfur, sulfate, and S-methylcysteine were altered by the sulfur treatment in both genotypes. The concentration of total cysteine and extractible globulins was increased specifically in SMARC1N-PN1. Proteomic analysis identified arcelin-like protein 4, lipoxygenase-3, albumin-2, and alpha amylase inhibitor beta chain as having increased levels under high sulfur conditions. Lipoxygenase-3 accumulation was sensitive to sulfur nutrition only in SMARC1N-PN1. Under field conditions, both SARC1 and SMARC1N-PN1 exhibited a slight increase in yield in response to sulfur treatment, typical for common bean.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Mark Sandercock
- Cereal Research Centre Morden, Agriculture and Agri-Food CanadaCanada, Morden, MB, Canada
| | - Ronald Beyaert
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kenneth L. Conn
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Anfu Hou
- Cereal Research Centre Morden, Agriculture and Agri-Food CanadaCanada, Morden, MB, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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38
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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39
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Betti M, García-Calderón M, Pérez-Delgado CM, Credali A, Pal'ove-Balang P, Estivill G, Repčák M, Vega JM, Galván F, Márquez AJ. Reassimilation of ammonium in Lotus japonicus. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5557-66. [PMID: 24948681 DOI: 10.1093/jxb/eru260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review summarizes the most recent results obtained in the analysis of two important metabolic pathways involved in the release of internal sources of ammonium in the model legume Lotus japonicus: photorespiratory metabolism and asparagine breakdown mediated by aparaginase (NSE). The use of photorespiratory mutants deficient in plastidic glutamine synthetase (GS2) enabled us to investigate the transcriptomics and metabolomic changes associated with photorespiratory ammonium accumulation in this plant. The results obtained indicate the existence of a coordinate regulation of genes involved in photorespiratory metabolism. Other types of evidence illustrate the multiple interconnections existing among the photorespiratory pathway and other processes such as intermediate metabolism, nodule function, and secondary metabolism in this plant, all of which are substantially affected in GS2-deficient mutants because of the impairment of the photorespiratory cycle. Finally, the importance of asparagine metabolism in L. japonicus is highlighted because of the fact that asparagine constitutes the vast majority of the reduced nitrogen translocated between different organs of this plant. The different types of NSE enzymes and genes which are present in L. japonicus are described. There is a particular focus on the most abundant K(+)-dependent LjNSE1 isoform and how TILLING mutants were used to demonstrate by reverse genetics the importance of this particular isoform in plant growth and seed production.
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Affiliation(s)
- Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Carmen M Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Alfredo Credali
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Peter Pal'ove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Mánesova 23, SK-04001 Košice, Slovak Republic
| | - Guillermo Estivill
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Miroslav Repčák
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Mánesova 23, SK-04001 Košice, Slovak Republic
| | - José M Vega
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Francisco Galván
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
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40
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Zhang D, Kan G, Hu Z, Cheng H, Zhang Y, Wang Q, Wang H, Yang Y, Li H, Hao D, Yu D. Use of single nucleotide polymorphisms and haplotypes to identify genomic regions associated with protein content and water-soluble protein content in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1905-15. [PMID: 24952096 DOI: 10.1007/s00122-014-2348-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/07/2014] [Indexed: 06/03/2023]
Abstract
KEY MESSAGE Four major SPC-specific loci were identified, and these accounted for 8.5-15.1 % of the phenotypic variation, thus explaining why certain soybean varieties have a high PC but a low SPC. Water-soluble protein content (SPC) is a critical factor in both food quality and the production of isolated soybean proteins. However, few data are available regarding the genetic control and the mechanisms contributing to elevated SPC. In this study, a soybean collection of 192 accessions from a wide geographic range was used to identify genomic regions associated with soybean protein content (PC) and SPC using an association mapping approach employing 1,536 SNP makers and 232 haplotypes. The diverse panel revealed a large genetic variation in PC and SPC. Association mapping was performed using three methods to minimize false-positive associations. This resulted in 4/8 SNPs and 3/6 haplotypes that were significantly associated with soybean PC/SPC in two or more environments based on the mixed model. An SNP that was highly significantly associated with PC, BARC-021267-04016, was localized 0.28 cM away from a published glycinin gene, G7, and was detected across all four environments. Four major SPC-specific loci, BARC-029149-06088, BARC-018023-02499, BARC-041663-08059 and haplotype 15 (hp15), were stably identified on chromosomes five and eight and explained 8.5-15.1 % of the phenotypic variation. Moreover, a glutelin type-B 2-like gene was identified on chromosome eight and may be related to soybean protein solubility. These markers, which are located in previously reported QTL, reconfirmed previous findings and may be important targets for the identification of protein-related genes. These novel SNPs and haplotypes are important for further understanding the genetic basis of PC and SPC. In addition, by comparing the correlation and genetic loci between PC and SPC, we provide new insights into why certain soybean varieties have a high protein content but a low SPC.
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Affiliation(s)
- Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China,
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Curtis T, Halford NG. Food security: the challenge of increasing wheat yield and the importance of not compromising food safety. THE ANNALS OF APPLIED BIOLOGY 2014; 164:354-372. [PMID: 25540461 PMCID: PMC4240735 DOI: 10.1111/aab.12108] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/06/2013] [Accepted: 12/11/2013] [Indexed: 05/03/2023]
Abstract
Current wheat yield and consumption is considered in the context of the historical development of wheat, from early domestication through to modern plant breeding, the Green Revolution and wheat's place as one of the world's most productive and important crops in the 21st Century. The need for further improvement in the yield potential of wheat in order to meet current and impending challenges is discussed, including rising consumption and the demand for grain for fuel as well as food. Research on the complex genetics underlying wheat yield is described, including the identification of quantitative trait loci and individual genes, and the prospects of biotechnology playing a role in wheat improvement in the future are discussed. The challenge of preparing wheat to meet the problems of drought, high temperature and increasing carbon dioxide concentration that are anticipated to come about as a result of climate change is also reviewed. Wheat yield must be increased while not compromising food safety, and the emerging problem of processing contaminants is reviewed, focussing in particular on acrylamide, a contaminant that forms from free asparagine and reducing sugars during high temperature cooking and processing. Wheat breeders are strongly encouraged to consider the contaminant issue when breeding for yield.
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Affiliation(s)
- T Curtis
- Plant Biology and Crop Science Department, Rothamsted ResearchHarpenden, Hertfordshirex, UK
| | - N G Halford
- Plant Biology and Crop Science Department, Rothamsted ResearchHarpenden, Hertfordshirex, UK
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Herman EM. Soybean seed proteome rebalancing. FRONTIERS IN PLANT SCIENCE 2014; 5:437. [PMID: 25232359 PMCID: PMC4153022 DOI: 10.3389/fpls.2014.00437] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/15/2014] [Indexed: 05/19/2023]
Abstract
The soybean seed's protein content and composition are regulated by both genetics and physiology. Overt seed protein content is specified by the genotype's genetic framework and is selectable as a breeding trait. Within the genotype-specified protein content phenotype soybeans have the capacity to rebalance protein composition to create differing proteomes. Soybeans possess a relatively standardized proteome, but mutation or targeted engineering can induce large-scale proteome rebalancing. Proteome rebalancing shows that the output traits of seed content and composition result from two major types of regulation: genotype and post-transcriptional control of the proteome composition. Understanding the underlying mechanisms that specifies the seed proteome can enable engineering new phenotypes for the production of a high-quality plant protein source for food, feed, and industrial proteins.
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Affiliation(s)
- Eliot M. Herman
- *Correspondence: Eliot M. Herman, School of Plant Sciences, BIO5 Institute, University of Arizona, BIO5 Institute Room 249, 1657 East Helen Street, Tucson, AZ 85721-0240, USA e-mail:
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43
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Gálvez-Valdivieso G, Alamillo JM, Fernández J, Pineda M. Molecular characterization of PVAS3: an asparagine synthetase gene from common bean prevailing in developing organs. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1484-1490. [PMID: 23846186 DOI: 10.1016/j.jplph.2013.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 06/02/2023]
Abstract
In common bean, asparagine synthetase (AS; EC 6.3.5.4) is encoded by three members of a multigene family called PVAS1, PVAS2 and PVAS3. Two of these genes, PVAS1 and PVAS2, have been extensively studied, but little is known about PVAS3, remaining unclear whether PVAS3 function is redundant to the other AS or if it plays a specific role in Phaseolus vulgaris metabolism. In this work, we used a molecular approach to characterize PVAS3 expression and to gain some knowledge about its physiological function. We showed that, in contrast to PVAS1 and PVAS2, PVAS3 was expressed in all organs analyzed. Interestingly, PVAS3 was the AS gene most highly expressed in nodules, leaves and pods at the earliest stages of development, and its expression decreased as these organs developed. Expression of PVAS3 parallels the accumulation of AS protein and the asparagine content during the earliest stages of nodule, leaf and pod development, suggesting an important role for PVAS3 in the synthesis of asparagine in that period. Furthermore, PVAS3 was not repressed by light, as most class-II AS genes. Surprisingly, fertilization of nodulated plants with nitrate or ammonium, conditions that induce PVAS1 and PVAS2 and the shift from ureides to amide synthesis, repressed the expression of PVAS3 in nodules and roots. The possible implications of this regulation are discussed.
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Affiliation(s)
- Gregorio Gálvez-Valdivieso
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo del Campus de Excelencia Internacional Agroalimentario (ceiA3), Instituto Andaluz de Biotecnología, Campus de Rabanales, Edif. C-6, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain.
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Withana-Gamage TS, Hegedus DD, Qiu X, McIntosh T, Wanasundara JPD. Structural and physicochemical property relationships of cruciferin homohexamers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:5848-5859. [PMID: 23738812 DOI: 10.1021/jf400559x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Heteromeric cruciferin from wild type (WT) Arabidopsis thaliana and homomeric cruciferin CRUA, CRUB, and CRUC composed of identical subunits obtained from double-knockout mutant lines were investigated for their structural and physicochemical properties. A three-step chromatographic procedure allowed isolation of intact cruciferin hexamers with high purity (>95%). FT-IR and CD analysis of protein secondary structure composition revealed that all cruciferins were folded into higher order structures consisting of 44-50% β-sheets and 7-9% α-helices. The structural and physicochemical properties of homohexameric CRUC deviated from that of CRUA and CRUB and exhibited a compact, thermostable, and less hydrophobic structure, confirming the predictions made using 3D homology structure models.
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45
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Liao D, Cram D, Sharpe AG, Marsolais F. Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds. FRONTIERS IN PLANT SCIENCE 2013; 4:60. [PMID: 23532826 PMCID: PMC3606967 DOI: 10.3389/fpls.2013.00060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/04/2013] [Indexed: 05/29/2023]
Abstract
Common bean (Phaseolus vulgaris) and black gram (Vigna mungo) accumulate γ-Glutamyl-S-methylcysteine and γ-Glutamyl-methionine in seed, respectively. Transcripts were profiled by 454 pyrosequencing data at a similar developmental stage coinciding with the beginning of the accumulation of these metabolites. Expressed sequence tags were assembled into Unigenes, which were assigned to specific genes in the early release chromosomal assembly of the P. vulgaris genome. Genes involved in multiple sulfur metabolic processes were expressed in both species. Expression of Sultr3 members was predominant in P. vulgaris, whereas expression of Sultr5 members predominated in V. mungo. Expression of the cytosolic SERAT1;1 and -1;2 was approximately fourfold higher in P. vulgaris while expression of the plastidic SERAT2;1 was twofold higher in V. mungo. Among BSAS family members, BSAS4;1, encoding a cytosolic cysteine desulfhydrase, and BSAS1;1, encoding a cytosolic O-acetylserine sulphydrylase were most highly expressed in both species. This was followed by BSAS3;1 encoding a plastidic β-cyanoalanine synthase which was more highly expressed by 10-fold in P. vulgaris. The data identify BSAS3;1 as a candidate enzyme for the biosynthesis of S-methylcysteine through the use of methanethiol as substrate instead of cyanide. Expression of GLC1 would provide a complete sequence leading to the biosynthesis of γ-Glutamyl-S-methylcysteine in plastids. The detection of S-methylhomoglutathione in P. vulgaris suggested that homoglutathione synthetase may accept, to some extent, γ-Glutamyl-S-methylcysteine as substrate, which might lead to the formation of S-methylated phytochelatins. In conclusion, 454 sequencing was effective at revealing differences in the expression of sulfur metabolic genes, providing information on candidate genes for the biosynthesis of distinct sulfur amino acid γ-Glutamyl dipeptides between P. vulgaris and V. mungo.
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Affiliation(s)
- Dengqun Liao
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
| | - Dustin Cram
- National Research Council CanadaSaskatoon, SK, Canada
| | | | - Frédéric Marsolais
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
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Credali A, García-Calderón M, Dam S, Perry J, Díaz-Quintana A, Parniske M, Wang TL, Stougaard J, Vega JM, Márquez AJ. The K+-Dependent Asparaginase, NSE1, is Crucial for Plant Growth and Seed Production in Lotus japonicus. ACTA ACUST UNITED AC 2012; 54:107-18. [DOI: 10.1093/pcp/pcs156] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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